Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_110806871.1 C8J30_RS16150 ATP-binding cassette domain-containing protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_003217355.1:WP_110806871.1 Length = 259 Score = 253 bits (645), Expect = 4e-72 Identities = 132/254 (51%), Positives = 180/254 (70%), Gaps = 4/254 (1%) Query: 11 ASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 A+ +L +D+HK +G EVLKG+ L + +V++++G+SGSGK+T LRC+N LE G Sbjct: 6 ATDLVLSAQDIHKSFGAQEVLKGITLGARNHDVISILGTSGSGKSTFLRCLNCLEVPNSG 65 Query: 71 QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVK 130 + + GE I + NG+ ++ I + R GM FQQFNL+ H T L+NV G ++VK Sbjct: 66 SVAVHGEEIVFR--NGRI--GDQRQIERLRRHLGMVFQQFNLWTHRTVLENVMEGPVQVK 121 Query: 131 KLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSA 190 ++ K EA LAE L RVGL +R HYP LSGGQQQRVAIARA+AM P ++LFDE TSA Sbjct: 122 RMPKAEARDLAEGLLARVGLADRMGHYPAMLSGGQQQRVAIARALAMEPDVILFDEPTSA 181 Query: 191 LDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFER 250 LDPELVGEVL V++ LA +G TM++VTHEM FA +VS ++VF+N+GRI EQGPP++LF+ Sbjct: 182 LDPELVGEVLKVMQDLAAEGRTMIVVTHEMAFARDVSTEVVFLNEGRIAEQGPPEKLFDH 241 Query: 251 PQSPRLAEFLKNTR 264 P++ A F+ TR Sbjct: 242 PETEVFARFISKTR 255 Lambda K H 0.319 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 198 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 265 Length of database: 259 Length adjustment: 25 Effective length of query: 240 Effective length of database: 234 Effective search space: 56160 Effective search space used: 56160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory